Difference between revisions of "Cluster by shortest path (analysis)"
From BioUML platform
(Automatic synchronization with BioUML) |
(Automatic synchronization with BioUML) |
||
| (12 intermediate revisions by one user not shown) | |||
| Line 1: | Line 1: | ||
| − | This analysis allows you to make a cluster of genes/molecules upstream or downstream or both by taking reactions and all intermediate molecules from a specified search collection | + | ;Analysis title |
| + | :[[File:Molecular-networks-Cluster-by-shortest-path-icon.png]] Cluster by shortest path | ||
| + | ;Provider | ||
| + | :[[geneXplain GmbH]] | ||
| + | ;Class | ||
| + | :{{Class|biouml.plugins.keynodes.ShortestPathClustering}} | ||
| + | ;Plugin | ||
| + | :[[Biouml.plugins.keynodes (plugin)|biouml.plugins.keynodes (Master regulator node analysis plugin)]] | ||
| + | |||
| + | ==== Description ==== | ||
| + | This analysis allows you to make a cluster of genes/molecules upstream or downstream or both by taking reactions and all intermediate molecules using shortest paths from a specified search collection. | ||
==== Parameters: ==== | ==== Parameters: ==== | ||
| Line 9: | Line 19: | ||
* '''Display intermediate molecules''' – Output the diagram with the direct reactions and all intermediate molecules | * '''Display intermediate molecules''' – Output the diagram with the direct reactions and all intermediate molecules | ||
* '''Search collection''' – Collection containing reactions | * '''Search collection''' – Collection containing reactions | ||
| + | * '''Custom search collection''' – Path to the custom search collection | ||
* '''Species''' – Species to which analysis should be confined | * '''Species''' – Species to which analysis should be confined | ||
* '''Output name''' – Output name. | * '''Output name''' – Output name. | ||
| Line 14: | Line 25: | ||
[[Category:Analyses]] | [[Category:Analyses]] | ||
[[Category:Molecular networks (analyses group)]] | [[Category:Molecular networks (analyses group)]] | ||
| + | [[Category:GeneXplain analyses]] | ||
| + | [[Category:Autogenerated pages]] | ||
Latest revision as of 18:15, 9 December 2020
- Analysis title
Cluster by shortest path
- Provider
- geneXplain GmbH
- Class
ShortestPathClustering- Plugin
- biouml.plugins.keynodes (Master regulator node analysis plugin)
[edit] Description
This analysis allows you to make a cluster of genes/molecules upstream or downstream or both by taking reactions and all intermediate molecules using shortest paths from a specified search collection.
[edit] Parameters:
- Molecules collection – Input the collection of molecules/genes
- Input size (expert) – Size of input list
- Search direction – Direction to perform search in (either upstream, downstream reactions or both directions)
- Max radius – Maximal search radius
- Display intermediate molecules – Output the diagram with the direct reactions and all intermediate molecules
- Search collection – Collection containing reactions
- Custom search collection – Path to the custom search collection
- Species – Species to which analysis should be confined
- Output name – Output name.
